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Abstract:
Most functional RNA molecules have characteristic secondary structures that
are highly conserved in evolution. Here we present a method for computing
the consensus structure of a set aligned RNA sequences taking into
account both thermodynamic stability and sequence covariation. Comparison
with phylogenetic structures of rRNAs shows that a reliability of
prediction of more than 80% is achieved for only five related sequences.
As an application we show that the Early Noduline mRNA contains significant
secondary structure that is supported by sequence covariation.
Keywords:
RNA secondary structure prediction,
conserved substructures, compensatory mutations
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